IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: In high-throughput projects aiming to identify rare positives using a binary assay, smart-pooling constitutes an appealing strategy liable of significantly reducing the number of tests while correcting for experimental noise. In order to perform simulations for choosing an appropriate set of pools, and later to interpret the experimental results, the pool outcomes must be ‘decoded’. The intuitive aim is clearly to identify the positives that gave rise to an observation, whether real or simulated. However, this goal is not well-formalized and has been the focus of very few studies. Results: We first provide a clear combinatorial formalization of the ‘decoding problem’. We then present interpool, an exact algorithm to solve this problem. An efficient implementation is freely available. Its usefulness is illustrated in the context of yeast-two-hybrid interactome mapping with the Shifted Transversal Design. Availability: The implementation, licensed under the GNU GPL, can be downloaded from http://www-timc.imag.fr/Nicolas.Thierry-Mieg/ Contact: nicolas.thierry-mieg@imag.fr Supplementary information: Supplementary data are available at Bioinformatics online.